Contacts of the strand formed by residues 218 - 226 (chain D) in PDB entry 5DST
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 218 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D PRO* 4.4 1.6 - - - +
217D ASP* 1.3 82.6 + - - +
219D ALA* 1.3 63.2 + - - +
220D ALA* 3.6 27.4 - - - +
222D TYR* 5.0 3.2 + - - -
277D GLU* 3.5 32.0 + - - +
278D VAL 3.5 9.0 - - - +
279D ASP* 5.2 6.7 - - + +
280D ILE* 4.6 3.7 - - - +
312D ASN* 5.8 4.2 + - - +
313D ILE* 3.7 6.6 - - - +
314D GLU* 2.8 70.1 + - + +
316D THR* 4.0 21.3 - - + -
349I ARG* 5.8 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D TRP* 4.3 11.9 - - + -
191D LEU* 4.2 20.2 - - + -
218D ARG* 1.3 81.7 + - - +
220D ALA* 1.3 63.9 + - - +
276D LYS 4.5 0.2 - - - -
277D GLU* 3.6 0.9 - - - +
278D VAL* 2.8 43.4 + - + -
280D ILE* 5.1 0.2 - - + -
312D ASN 3.4 7.4 - - - -
313D ILE* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D LEU* 4.6 2.0 - - - +
218D ARG* 3.6 21.1 - - - +
219D ALA* 1.3 77.0 - - - +
221D LEU* 1.3 59.9 + - - +
222D TYR* 3.7 25.6 - - + +
274D LEU* 3.9 9.6 - - + -
276D LYS 3.2 7.4 - - - +
277D GLU* 4.8 1.6 - - - -
311D PHE* 3.2 7.9 - - - +
312D ASN* 3.0 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D CYS* 4.1 31.9 - - - +
191D LEU* 4.1 11.2 - - + +
192D PHE* 4.3 19.1 - - + -
220D ALA* 1.3 74.1 - - - +
222D TYR* 1.3 62.8 + - - +
274D LEU* 3.7 3.8 - - - +
275D ILE* 2.8 50.5 + - + +
276D LYS* 2.8 25.6 + - + +
290D PHE* 4.9 6.1 - - + -
309D THR* 4.1 14.4 - - - +
310D TYR 3.4 21.3 - - - +
311D PHE* 4.1 8.3 - - + -
358D ILE* 5.9 1.1 - - + -
360D MET* 5.0 3.6 - - - -
372D PHE* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D ARG* 5.0 3.3 + - - -
220D ALA* 3.7 32.3 - - + +
221D LEU* 1.3 75.0 - - - +
223D VAL* 1.3 64.5 + - - +
272D ALA* 4.4 7.2 - - + -
273D CYS* 3.3 18.2 - - - +
274D LEU* 3.6 30.7 - - + +
275D ILE* 4.2 3.6 - - - -
309D THR* 3.1 30.7 - - - +
310D TYR* 2.8 56.3 + + + +
312D ASN* 3.6 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D TYR* 1.3 73.1 - - - +
224D VAL* 1.3 69.7 + - - +
272D ALA* 3.5 2.6 - - - +
273D CYS* 2.9 33.3 + - + +
275D ILE* 3.5 31.6 - - + -
294D PHE* 4.0 23.3 - - + -
296D LEU* 3.6 7.6 - - + +
307D LEU* 4.7 19.5 - - + -
308D VAL 3.2 8.1 - - - +
309D THR* 3.7 24.5 - - + -
310D TYR* 5.1 0.4 - - - -
358D ILE* 4.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D VAL* 1.3 82.3 - - - +
225D ALA* 1.3 65.2 + - - +
226D ILE* 3.9 8.1 - - + -
268D VAL* 3.5 39.9 - - + -
270D THR* 3.7 4.0 - - - +
271D ASN 3.3 19.3 - - - +
272D ALA* 3.8 13.9 - - + -
296D LEU* 3.7 8.3 - - - -
307D LEU* 3.3 6.8 - - - +
308D VAL* 2.8 38.4 + - + +
310D TYR* 4.3 14.1 - - + -
328D PRO* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D VAL* 1.3 73.3 - - - +
226D ILE* 1.3 66.8 + - - +
269D VAL* 2.9 26.3 + - - +
270D THR* 3.0 30.4 + - + -
296D LEU* 3.6 5.8 - - + +
304D VAL* 3.9 24.9 - - + -
306D ALA 3.4 5.8 - - - +
307D LEU* 3.9 11.9 - - + -
354D ILE* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D VAL* 3.9 12.1 - - + -
225D ALA* 1.3 80.3 - - - +
227D GLU* 1.3 60.4 + - - +
228D ASP* 3.8 28.3 - - + +
263D VAL* 4.0 17.3 - - + -
267D GLN* 3.3 24.2 - - - +
268D VAL* 3.9 12.3 - - + -
269D VAL* 4.1 6.1 - - - -
303D TYR 4.2 0.4 - - - -
304D VAL* 3.3 4.6 - - - -
305D HIS 2.9 23.6 + - - -
306D ALA* 2.9 28.9 + - + +
308D VAL* 3.6 32.5 - - + -
339D VAL* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il